It should be documented that mysqlnd is a new development and doesn't implement magic quotes. PDO is a new development too, and doesn't implement magic quotes too. What can be done is adding a php_error_docref(E_WARNING) at MINIT/RINIT which will tell the developer that if mysqlnd is active and magic_quotes is set that it won't work with mysqli. Also a warning can be thrown at every mysqli call.

Getting quite unsure about the won't fix after discussion with Johannes. Johannes is correct in arguing that the silent removal of a deprecated feature could break apps unexpectedly, which is bad because magic quotes has some security impact.
Maybe adding magic quotes (although they are deprecated) to mysqlnd and throwing a deprecation warning would be best?
Phillip, thoughts? You re-opened it. Not sure if you noticed I had changed the category/package: Did you intend to re-open as docs or code issue?